Former MBTA general manager Daniel Grabauskas said the transit authority tried to keep his $327,487 severance secret when he agreed to resign two years ago, but he refused to sign an agreement keeping it confidential.

As the Globe reported last month, the MBTA and other state agencies have sworn dozens of workers to secrecy as part of lucrative severance and settlement agreements since 2005, according to documents the agencies provided to the Globe.

The Globe initially cited Grabauskas’s severance agreement as one of the confidential pacts signed by the MBTA, based on a copy of the document the agency provided to the Globe. But the MBTA later acknowledged it sent the Globe an early draft of the document by mistake and that the confidentiality clause was removed from the final version at Grabauskas’s insistence.

He recalled telling the MBTA’s lawyer that “any attempt to keep the use of public funds secret is at best silly, injuring public confidence, and at worst simply illegal.’’

Grabauskas was forced to resign in August 2009 after the Patrick administration publicly questioned his leadership. He said he thought the MBTA was trying to avoid the embarrassment of paying him so much to leave before his contract ended.

Grabauskas’s attorney in the negotiations, Mark Ventola, confirmed his client’s account and added that agency officials did not say why they wanted the secrecy clause.

MBTA General Manager Daniel Grabauskas is accusing the Patrick administration of dragging its feet in response to e-mail messages sent to the T by a Department of Correction employee who allegedly used derogatory and obscene language to refer to Grabauskas, who is gay.

In a string of e-mails, DOC paralegal Mark Roberts allegedly used profanity and anti-gay epithets to insult Grabauskas, whom he accused of not responding to his complaints of poor commuter rail service, according to copies of the messages reviewed by the Herald.

Embattled MBTA boss Daniel Grabauskas, under fierce pressure from Gov. Deval Patrick, finally agreed to step down last night, but his ouster came at a steep price in the form of a golden parachute worth almost $330,000.

Grabauskas’ forced resignation comes after a long, bitter siege by the Patrick adminstration, which had been sniping at the T general manager over safety and service issues.

His decision comes after a week of heavy criticism from several members of the MBTA board of directors and Transportation Secretary James Aloisi.

Board members Janice Loux, Ferdinand Alvaro and Darnell Williams sent a letter (PDF) to Aloisi questioning Grabauskas’ commitment following an NTSB crash report that found the MBTA lacked “a culture of safety.”

Grabauskas was on scheduled furlough and unavailable for comment on the day the report was released. Aloisi publicly chastised Grabauskas, saying, “You are never on furlough when you are a high government official.”

Four other board members sent Aloisi an impassioned letter in defense of Grabauskas (PDF) on Thursday.

“We have found him responsible, innovative, and focused on customer service and safety,” the letter said. “General Manager Grabauskas has had, and continues to have, our confidence.” The letter was signed by board members Willie Davis, Grace Shepard, Frank Chin and Baron Martin.

Grabauskas called Aloisi’s comments “political.” He held the same opinion of the first MBTA board members’ letter critical of his performance. Grabauskas and Aloisi’s working relationship — initially cordial when Aloisi took the helm at the Executive Office of Transportation — has grown increasingly caustic over the past weeks.

Aloisi declined to comment on Grabauskas’s contract non-renewal announcement Thursday. He told the Boston Globe on Wednesday, “This is about getting it right. And attempts to change the discussion, frankly, by throwing politics into it or throwing personality into it, that’s not right, it’s not fair.”

Gov. Deval Patrick stoked the controversy Wednesday. “We’ve had two serious accidents within a short time frame,” he said, referring to the 2008 and 2009 crashes on the MBTA’s Green Line. “We’ve got serious fiscal issues at the T, so serious that even with some infusion of new state dollars they are still considering a fare increase, something that could not come at a worse time.”

Patrick declined to note that his own transportation secretary, Aloisi, directed Grabauskas to increase T fares. The fare hike could go into effect this September. Aloisi serves as chairman of the MBTA board of directors and has frequently told reporters that a fare increase is necessary as a “long-term solution” to put the T in “better financial shape for a period of two to three years.”

MBTA_General_Manager_Dan_Grabauskas: Hi, this is Dan Grabauskas, and I will be happy to answer your questions for the next hour or so. So let's get started.

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New HART Boss Fired After Crashes, Financial Troubles

CB: One of the first results of a Google search for Grabauskas' name is an August 2009 Boston Globe article with the ominous headline "Embattled MBTA chief resigns." The story notes that Grabauskas is a Republican appointed by then-Massachusetts Gov. Mitt Romney, left amid lots of problems and political squabbles.

The change comes after (then-new Gov. Deval) Patrick questioned the management of the public transit agency in the wake of two Green Line crashes and financial troubles. But Grabuaskas's backers, who include legislative leaders and members of the T board, have praised his work leading the chronically troubled transit agency and say Patrick's campaign to remove him is purely political.

UPDATE Hui said HART already did due diligence on Grabauskas' background — including a "lot of articles" about him leaving the MBTA — and determined that his ouster was due to a change in the governor's office.

Interim executive director Toru Hamayasu had applied for the position but was not selected. He'll be in charge until a permanent chief is here, and then he'll continue in a "senior leadership position" thereafter.